Has David Cameron got a Boris Johnson problem? Today's Guardian reveals how the mayor of London's deputy for policing, Kit Malthouse, believes the Tory team has taken control of the priorities of the Metropolitan police – from the Home Office and the beleaguered Yard itself. Not brilliant reading for the police, nor Cameron: there's a cockiness amid the candour from Malthouse – a mixture that is almost Johnsonesque. It smacks of triumphalism, very much not the style required at Tory HQ less than nine months before a general election.

Cameron and Johnson go back a long way, they've been friends and fluctuating rivals right back to their school days, but now they are the two most powerful Conservatives in the country, which makes their relationship more than an Eton trifle. And, since Johnson announced that he was a candidate for mayor of London in July 2007, the dynamic has shifted in at least three ways.

• Phase one: Johnson solves a problem for Cameron. It is easy to forget that Boris's candidature wasn't just (if you choose to view it this way) an ego-fuelled lark by a moptop maverick. It got Cameron out of a hole. The Tory leader wanted a celebrity candidate for mayor – Greg Dyke (as a joint candidate with the Liberal Democrats), Lord Sebastian Coe, Lord John Stevens, Sir John Major, Anne Robinson. Wasn't Jeremy Clarkson in the frame at one point? But he got none of them. Johnson was a celebrity and a Tory. And then he went and won – beating an incumbent, populist mayor, showing that posh Tories could win, with a final vote, albeit on a different voting system, not much different from Obama's near-landslide.

• Phase two: Johnson becomes a problem because he is so hopeless. The first few months of the Johnson reign at City Hall were pretty disastrous. Poor appointments, early resignations – James McGrath, Tim Parker, Ray Lewis, a general air of shambolism. Not a good advert for Tory rule. No narrative.

• Phase three: Johnson becomes a problem because he starts to be successful. The stain of incompetence has not been entirely eroded. Ian Clement, a deputy mayor, quit in June over his expenses claims and Malthouse's intervention does him no favours. But Mayor Johnson has found his voice – different, generally funnier and occasionally punchier than Cameron's. Unbelievably, he has refused to rule out a return to Westminster and still dreams of becoming prime minister. On the City (defending big bonuses, resisting financial regulation as he did yesterday in Brussels), on airport expansion, to some extent on immigration (more for it than the Cameroons), he has policies at odds with the national leadership.

It is hard to say whether unpopular Johnson policies would adversely affect the Tory vote at a general election. It is probable that if he had continued as he started, it could have. Johnson isn't in that position now. He has a power base and makes waves, while he is, for a few more months at least, the Tory with the biggest electoral mandate. Cameron can't rebuke him, or withdraw the whip, or (realistically) campaign against him. All he can do is tolerate him.